[gmx-users] atomnumber=-12345

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Thu Jan 21 03:36:18 CET 2010


Might be a good idea to provide the input and output that generated the
error.

 

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Itamar Kass
Sent: Thursday, 21 January 2010 11:13 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] atomnumber=-12345

 

Hi,

After one of my simulation had crashed, I had used gmxdump to look into
it.  What stoke me was the all atoms have the same atomnumer:
 atom[     0]={type=  0, typeB=  0, ptype=    Atom, m= 1.40067e+01, q=
1.29000e-01, mB= 1.40067e+01, qB= 1.29000e-01, resnr=    0,
atomnumber=-12345}
         atom[     1]={type=  1, typeB=  1, ptype=    Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr=
0, atomnumber=-12345}
         atom[     2]={type=  1, typeB=  1, ptype=    Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr=
0, atomnumber=-12345}
         atom[     3]={type=  1, typeB=  1, ptype=    Atom, m=
1.00800e+00, q= 2.48000e-01, mB= 1.00800e+00, qB= 2.48000e-01, resnr=
0, atomnumber=-12345}
         atom[     4]={type=  2, typeB=  2, ptype=    Atom, m=
1.30190e+01, q= 1.27000e-01, mB= 1.30190e+01, qB= 1.27000e-01, resnr=
0, atomnumber=-12345}
         

and so on...

I wonder if someone knows what the origin of this error and how to over
come it?

In addition, it is vary strange that the simulation run for 100ps before
it crashed. 

All the best,
Itamar.


-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut 

=========================================== 
| Itamar Kass, Ph.D. 
| Postdoctoral Research Fellow 
| 
| Department of Biochemistry and Molecular Biology 
| Building 77 Clayton Campus 
| Wellington Road 
| Monash University, 
| Victoria 3800 
| Australia 
| 
| Tel: +61 3 9902 9376 
| Fax: +61 3 9902 9500 
| E-mail: Itamar.Kass at med.monash.edu.au 
============================================ 

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